Extensive identification and analysis of conserved small ORFs in animals
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Abstract
BACKGROUND: There is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential developmental or physiological roles for a few of the encoded peptides (micropeptides), but genome-wide experimental or computational identification of functional sORFs remains challenging. RESULTS: Here, we expand our previously developed method and present results of an integrated computational pipeline for the identification of conserved sORFs in human, mouse, zebrafish, fruit fly, and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on amino acid (rather than nucleotide) sequence, we identify about 2,000 novel small ORFs located in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. The encoded peptides have little homology to known proteins and are enriched in disordered regions and short linear interaction motifs. Published ribosome profiling data indicate translation of more than 100 novel sORFs, and mass spectrometry data provide evidence for more than 70 novel candidates. CONCLUSIONS: Taken together, we identify hundreds of previously unknown conserved sORFs in major model organisms. Our computational analyses and integration with experimental data show that these sORFs are expressed, often translated, and sometimes widely conserved, in some cases even between vertebrates and invertebrates. We thus provide an integrated resource of putatively functional micropeptides for functional validation in vivo.
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- Authors
- Mackowiak, S. D., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M., & Obermayer, B.
- Affiliations
- Max Delbrück Center (DE)
- Corresponding author
- Obermayer, Benedikt
- ORCID
- Venue
- Genome Biology
- Published
- 2015-09-14
- Volume
- 16
- Issue
- 1
- Pages
- 179-179
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4568590
- OpenAlex
- W2154350719
- Cited by
- 227
- References
- 104
- Citations by year
- 2026: 8 · 2025: 21 · 2024: 23 · 2023: 29 · 2022: 20 · 2021: 26 · 2020: 21 · 2019: 11 · 2018: 27 · 2017: 25 · 2016: 10 · 2015: 6
- FWCI
- 9.85
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- small open reading frames, micropeptides, purifying selection, untranslated regions, non-coding transcripts, protein disorder, ribosome profiling, translation (biology), evolutionary conservation, model organisms
- MeSH terms
- Amino Acid Sequence, Animals, Exons, Humans, Peptides, Protein Biosynthesis, Open Reading Frames, Sequence Alignment, Conserved Sequence, Codon, Terminator, 3' Untranslated Regions, Amino Acid Motifs, Mice
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